Root Crons Not executing~

I have been bouncing back and forth on cpanel ticket # 177363
for over a week now - we ASSUMED the unit was just not sending out emails concerning the daily crons / cpbackup and upcp logwatch etc./.... this is not the case after careful inspection and resets of the times on the crons I watched as the time passed by for the unit to execute its root crons and it just blew past the times and never ran them ~
So I went and ran
run-parts /etc/cron.daily

surprise not only did it run that job it also sent the email to me as soon as it completed first time I had heard from the machine since its build~
So does anyone have an idea as to why this unit is just ignoring its crons?? its running user crons just fine~